CN108351917B - 用于高精度识别变体的系统和方法 - Google Patents

用于高精度识别变体的系统和方法 Download PDF

Info

Publication number
CN108351917B
CN108351917B CN201680054282.0A CN201680054282A CN108351917B CN 108351917 B CN108351917 B CN 108351917B CN 201680054282 A CN201680054282 A CN 201680054282A CN 108351917 B CN108351917 B CN 108351917B
Authority
CN
China
Prior art keywords
hla
patient
mers
type
reads
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
CN201680054282.0A
Other languages
English (en)
Chinese (zh)
Other versions
CN108351917A (zh
Inventor
J·Z·桑伯恩
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Nantomics LLC
Original Assignee
Nantomics LLC
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Nantomics LLC filed Critical Nantomics LLC
Publication of CN108351917A publication Critical patent/CN108351917A/zh
Application granted granted Critical
Publication of CN108351917B publication Critical patent/CN108351917B/zh
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/40Population genetics; Linkage disequilibrium
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10Sequence alignment; Homology search
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B45/00ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16CCOMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60In silico combinatorial chemistry

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Bioethics (AREA)
  • Library & Information Science (AREA)
  • Ecology (AREA)
  • Physiology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Computing Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
CN201680054282.0A 2015-08-25 2016-08-25 用于高精度识别变体的系统和方法 Active CN108351917B (zh)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562209858P 2015-08-25 2015-08-25
US62/209,858 2015-08-25
PCT/US2016/048768 WO2017035392A1 (en) 2015-08-25 2016-08-25 Systems and methods for high-accuracy variant calling

Publications (2)

Publication Number Publication Date
CN108351917A CN108351917A (zh) 2018-07-31
CN108351917B true CN108351917B (zh) 2022-03-08

Family

ID=58101056

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201680054282.0A Active CN108351917B (zh) 2015-08-25 2016-08-25 用于高精度识别变体的系统和方法

Country Status (13)

Country Link
US (2) US11393557B2 (ja)
EP (1) EP3341877B1 (ja)
JP (2) JP6533011B2 (ja)
KR (2) KR102211461B1 (ja)
CN (1) CN108351917B (ja)
AU (2) AU2016311444B2 (ja)
BR (1) BR112018003631A2 (ja)
CA (1) CA2996702C (ja)
HK (1) HK1257052A1 (ja)
IL (2) IL257724B (ja)
MX (1) MX2018002293A (ja)
RU (1) RU2018106934A (ja)
WO (1) WO2017035392A1 (ja)

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3280738A4 (en) 2015-04-08 2019-01-02 Nantomics, LLC Cancer neoepitopes
MX2018002293A (es) 2015-08-25 2018-09-05 Nantomics Llc Sistemas y métodos para las llamadas variantes de alta precisión.
KR20180087246A (ko) 2015-10-12 2018-08-01 난토믹스, 엘엘씨 네오에피토프의 반복적 발견 및 이에 대한 적응성 면역치료 및 방법
KR20180087244A (ko) 2015-10-12 2018-08-01 난토믹스, 엘엘씨 체크포인트 억제제에 대한 감도를 예측하는 msi 및 네오에피토프를 발견하기 위한 위한 시스템, 조성물 및 방법
AU2017217877A1 (en) 2016-02-12 2018-08-16 Nant Holdings Ip, Llc High-throughput identification of patient-specific neoepitopes as therapeutic targets for cancer immunotherapies
KR20180117227A (ko) 2016-03-24 2018-10-26 난트셀, 인크. 네오에피토프 제시를 위한 시퀀스들 및 시퀀스 배열들
KR20210010678A (ko) 2016-06-30 2021-01-27 난트 홀딩스 아이피, 엘엘씨 난트 암 백신
US10319465B2 (en) * 2016-11-16 2019-06-11 Seven Bridges Genomics Inc. Systems and methods for aligning sequences to graph references
AU2017362730B2 (en) 2016-11-21 2021-04-08 Nant Holdings Ip, Llc Fractal combination therapy
CN110214275B (zh) 2016-12-01 2022-12-06 南托米克斯有限责任公司 肿瘤抗原性加工和呈递
CN116983395A (zh) 2017-04-24 2023-11-03 河谷细胞有限公司 靶向性新表位载体及其方法
EP3933408A1 (en) 2017-05-30 2022-01-05 Nant Holdings IP LLC Circulating tumor cell enrichment using neoepitopes
CN111213210A (zh) * 2017-09-06 2020-05-29 河谷控股Ip有限责任公司 Hla组织匹配及用于其的方法
US11823773B2 (en) 2018-04-13 2023-11-21 Nant Holdings Ip, Llc Nant cancer vaccine strategies
TWI787500B (zh) 2018-04-23 2022-12-21 美商南特細胞公司 新抗原表位疫苗及免疫刺激組合物及方法
US11564980B2 (en) 2018-04-23 2023-01-31 Nantcell, Inc. Tumor treatment method with an individualized peptide vaccine
US20220108768A1 (en) * 2019-03-08 2022-04-07 Nantomics, Llc System and method for variant calling
CN112885406B (zh) * 2020-04-16 2023-01-31 深圳裕策生物科技有限公司 检测hla杂合性缺失的方法及系统
CN112289376B (zh) * 2020-10-26 2021-07-06 北京吉因加医学检验实验室有限公司 一种检测体细胞突变的方法及装置
CN114496077B (zh) * 2022-04-15 2022-06-21 北京贝瑞和康生物技术有限公司 用于检测单核苷酸变异和插入缺失的方法、设备和介质
WO2024106826A1 (ko) * 2022-11-16 2024-05-23 주식회사 세니젠 기준 서열 데이터와 타겟 및 비-타겟종의 교차검증을 활용한, PCR을 위한 K-mer 유전자 데이터 프로세싱 방법 및 그 장치

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102460155A (zh) * 2009-04-29 2012-05-16 考利达基因组股份有限公司 用于关于参考多核苷酸序列标注样本多核苷酸序列中的变异的方法和系统
CN103699819A (zh) * 2013-12-10 2014-04-02 深圳先进技术研究院 基于多步双向De Bruijn图的变长kmer查询的顶点扩展方法

Family Cites Families (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100261189A1 (en) * 2008-10-03 2010-10-14 Roche Molecular Systems, Inc. System and method for detection of HLA Variants
US20130267429A1 (en) * 2009-12-21 2013-10-10 Lawrence Livermore National Security, Llc Biological sample target classification, detection and selection methods, and related arrays and oligonucleotide probes
WO2011143231A2 (en) 2010-05-10 2011-11-17 The Broad Institute High throughput paired-end sequencing of large-insert clone libraries
CA2885058A1 (en) * 2012-10-08 2014-04-17 Spiral Genetics Inc. Methods and systems for identifying, from read symbol sequences, variations with respect to a reference symbol sequence
US9181583B2 (en) 2012-10-23 2015-11-10 Illumina, Inc. HLA typing using selective amplification and sequencing
EP3915369A1 (en) 2012-12-13 2021-12-01 CytRx Corporation Anthracycline formulations
WO2014116729A2 (en) 2013-01-22 2014-07-31 The Board Of Trustees Of The Leland Stanford Junior University Haplotying of hla loci with ultra-deep shotgun sequencing
WO2014197569A1 (en) 2013-06-05 2014-12-11 Cytrx Corporation Cytotoxic agents for the treatment of cancer
JP2015035212A (ja) * 2013-07-29 2015-02-19 アジレント・テクノロジーズ・インクAgilent Technologies, Inc. ターゲットシークエンシングパネルから変異を見つける方法
KR102386134B1 (ko) 2013-10-15 2022-04-12 리제너론 파마슈티칼스 인코포레이티드 고분별능 대립유전자 동정
NZ721908A (en) 2013-12-20 2022-12-23 Massachusetts Gen Hospital Combination therapy with neoantigen vaccine
EP3280738A4 (en) 2015-04-08 2019-01-02 Nantomics, LLC Cancer neoepitopes
MX2018002293A (es) 2015-08-25 2018-09-05 Nantomics Llc Sistemas y métodos para las llamadas variantes de alta precisión.
JP2019511903A (ja) 2016-02-19 2019-05-09 ナント ホールディングス アイピー エルエルシーNant Holdings IP, LLC 免疫原性調節の方法
KR20180118198A (ko) 2016-03-18 2018-10-30 난트셀, 인크. 수지상 세포 감염을 위한 멀티모달 벡터(multimodal vector for dendritic cell infection)
KR20210010678A (ko) 2016-06-30 2021-01-27 난트 홀딩스 아이피, 엘엘씨 난트 암 백신
CN111225673A (zh) 2017-09-06 2020-06-02 河谷细胞有限公司 亚德阿霉素组合治疗及方法

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102460155A (zh) * 2009-04-29 2012-05-16 考利达基因组股份有限公司 用于关于参考多核苷酸序列标注样本多核苷酸序列中的变异的方法和系统
CN103699819A (zh) * 2013-12-10 2014-04-02 深圳先进技术研究院 基于多步双向De Bruijn图的变长kmer查询的顶点扩展方法

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
De novo assembly and genotyping of variants using colored de Bruijn graphs;Zamin Iqbal et al.;《Nat Genet. Author manuscript》;20120801;第3-4,7,12-13页 *
Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers;Bilal Wajid et al.;《GENOMICS PROTEOMICS & BIOINFORMATICS》;20120430;第58-73页 *
整合多层次数据多方位解析和注释人类转录组;陈庚;《中国博士学位论文全文数据库 基础科学辑》;20141215;第2014年卷(第12期);第A006-6页 *

Also Published As

Publication number Publication date
JP6883180B2 (ja) 2021-06-09
AU2019201869A1 (en) 2019-04-11
IL263115B (en) 2020-06-30
KR102011440B1 (ko) 2019-08-16
KR102211461B1 (ko) 2021-02-03
KR20180058718A (ko) 2018-06-01
JP2019169177A (ja) 2019-10-03
US20220319640A1 (en) 2022-10-06
JP6533011B2 (ja) 2019-06-19
CA2996702A1 (en) 2017-03-02
EP3341877A4 (en) 2018-10-03
BR112018003631A2 (pt) 2018-09-25
IL263115A (en) 2018-12-31
CN108351917A (zh) 2018-07-31
HK1257052A1 (zh) 2019-10-11
EP3341877A1 (en) 2018-07-04
JP2018533111A (ja) 2018-11-08
CA2996702C (en) 2020-07-14
EP3341877B1 (en) 2023-05-10
US20180237949A1 (en) 2018-08-23
MX2018002293A (es) 2018-09-05
AU2016311444B2 (en) 2019-02-07
AU2016311444A1 (en) 2018-03-15
RU2018106934A (ru) 2019-09-26
US11393557B2 (en) 2022-07-19
WO2017035392A1 (en) 2017-03-02
RU2018106934A3 (ja) 2019-09-26
IL257724B (en) 2018-11-29
KR20190090022A (ko) 2019-07-31

Similar Documents

Publication Publication Date Title
CN108351917B (zh) 用于高精度识别变体的系统和方法
Tamames et al. SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline
CA2964902C (en) Ancestral human genomes
US10204208B2 (en) Systems and methods for genomic variant annotation
Brudno et al. Automated whole-genome multiple alignment of rat, mouse, and human
KR101542529B1 (ko) 대립유전자의 바이오마커 발굴방법
CN111213210A (zh) Hla组织匹配及用于其的方法
KR20140061223A (ko) 차세대 시퀀싱 데이터의 질병변이마커 검출 방법
WO2019047181A1 (zh) 基于低深度基因组测序进行基因分型的方法、装置及其用途
Pazhenkova et al. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria
US20210313012A1 (en) Difference-based genomic identity scores
Zhang et al. Positive selection and adaptive introgression of Haplotypes from Bos indicus improve the modern Bos taurus cattle
Baschal et al. Congruence as a measurement of extended haplotype structure across the genome
Villanea et al. ABO genetic variation in Neanderthals and Denisovans
Zemaitis et al. Determining international spread of novel B. 1.1. 523 SARS-CoV-2 lineage
Martinů et al. Host “cleansing zone” at secondary contact: a new pattern in host-parasite population genetics
Shokrof Large-Scale Analysis of Population Structural Variants Using Terabytes of SRA Sequencing Data
Ollé Vilanova et al. Population genetics meets phylogenetics: new insights into the relationships among members of the genus Euthynnus (family Scombridae)
Parejo Feuz et al. amelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap
Kacar Dissecting Tumor Clonality in Liver Cancer: A Phylogeny Analysis Using Computational and Statistical Tools
Levi Analysis of network-based module discovery algorithms from the perspective of biological enrichment
JP2008152592A (ja) 個体間の遺伝的非類似度の解析方法およびシステム
Fuellen Homology and phylogeny and their automated inference
Al-Khudhair Inter-and intra-population genetic variations in humans

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
GR01 Patent grant
GR01 Patent grant